The combination of nano sizes, large pore sizes and green synthesis is recognized as one of the most crucial and challenging problems in constructing metal-organic frameworks (MOFs). Herein, a water-based strategy is proposed for the synthesis of nanoscale hierarchical MOFs (NH-MOFs) with high crystallinity and excellent stability. This approach allows the morphology and porosity of MOFs to be fine tuned, thereby enabling the nanoscale crystal generation and a well-defined hierarchical system. The aqueous solution facilitates rapid nucleation kinetics, and the introduced modulator acts as a deprotonation agent to accelerate the deprotonation of the organic ligand as well as a structure-directing agent (SDA) to guide the formation of hierarchical networks. The as-synthesized NH-MOFs (NH-ZIF-67) were assessed as efficient adsorbents and heterogeneous catalysts to facilitate the diffusion of guest molecules, outperforming the parent microZIF-67. This study focuses on understanding the NH-MOF growth rules, which could allow tailor-designing NH-MOFs for various functions.